ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.3119C>G (p.Ser1040Cys)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001229615 SCV001402067 uncertain significance Chédiak-Higashi syndrome 2024-12-16 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 1040 of the LYST protein (p.Ser1040Cys). This variant is present in population databases (rs541176869, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with LYST-related conditions. ClinVar contains an entry for this variant (Variation ID: 956750). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Possibly Damaging". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002563729 SCV003539987 uncertain significance Inborn genetic diseases 2022-02-11 criteria provided, single submitter clinical testing The c.3119C>G (p.S1040C) alteration is located in exon 6 (coding exon 4) of the LYST gene. This alteration results from a C to G substitution at nucleotide position 3119, causing the serine (S) at amino acid position 1040 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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